Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KMT2D

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Large intestine; Colon
cell line
HCT116
tissue
Large intestine; Colon
disease state
Carcinoma; Colorectal
treatment
pSin-FOXD2 epxressing vector
chip antibody
ML4/KMT2D (Santa crz, sc-293217)

Sequenced DNA Library

library_name
GSM5904703
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cultured cells were collected by 0.25% Trypsin-EDTA (Gibco, 25200), then washed with DPBS. Crosslinked 6.0 or 10.0 × 106 HCT116 cells for 7 min at 37 °C with 1% formaldehyde. We perforemd FOXD2-flag or 6xHis ChIP with sonicated chromatin in RIPA buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 50 mM NaCl, 1% NP-40, 0.01% SDS, and 0.5% sodium deoxycholate, 1mM PMSF and 1X protease inhibitor cocktail) with 4μg of antibody; MLL4/KMT2D antibody (Santa crz, sc-293217) or Anti-6X His tag® antibody [HIS.H8] (Abcam, ab18184) or Monoclonal ANTI-FLAG® M2 antibody (Sigma-Aldrich, F1804). For histone ChIP using MNase without crosslinking method, we resuspended 1.0 x 106 HCT116 cells in 50ul of nuclei isolation buffer (Sigma-Aldrich, NUC101) and incubated on ice for 10 min. We then proceeded to MNase digestion with final concentration 2 units/μl (NEB, M0247), pre-clearing and immunoprecipitated chromatin in ChIP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, and 1 mM PMSF) with 2μg of antibody; H3K4me3 (Abcam, ab8580) or H3K4me1 (Abcam, ab8895) or H3K27ac (Abcam, ab4729).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
21159449
Reads aligned (%)
87.3
Duplicates removed (%)
11.7
Number of peaks
815 (qval < 1E-05)

hg19

Number of total reads
21159449
Reads aligned (%)
86.7
Duplicates removed (%)
11.9
Number of peaks
558 (qval < 1E-05)

Base call quality data from DBCLS SRA